Modified chitin-binding domain and use thereof

ABSTRACT

Compositions and methods are provided for reversibly binding chitin binding domain (CBD) to a chitin or equivalent substrate under non denaturing conditions. CBD is modified preferably by a mutation to achieve this change in properties. In one embodiment, an aromatic amino acid residue located in the binding cleft of the CBD was altered resulting in reversible binding affinity for substrate in select conditions. Creating a modified CBD with an altered binding affinity for substrate provides new uses for CBD not previously possible with unmodified CBD which binds irreversibly to chitin.

CROSS REFERENCE

This Application is a divisional application of U.S. application Ser.No. 10/375,913 filed Feb. 26, 2003, which gains priority fromProvisional Application Ser. No. 60/360,354 filed Feb. 28, 2002, each ofwhich is herein incorporated by reference.

BACKGROUND

The present invention relates to a modified chitin binding domain andmethods for making the same where the modification alters the propertiesof the chitin binding domain so that it becomes capable, under selectconditions, of elution from a substrate for which it has specificaffinity.

Although a number of different approaches to protein purification exist,the application of recombinant techniques to generating fusion proteinsfrom target proteins and substrate binding proteins (affinity tags) hasprovided efficient methods of separating target proteins from complexmixtures and/or large volumes. (LaVallie and McCoy, Curr. Opin.Biotechnol., 6:501-506 (1995), U.S. Pat. Nos. 5,834,247 and 5,643,758).Examples of substrate binding proteins include the chitin binding domain(CBD or ChBD) of chitinase which binds chitin substrate (U.S. Pat. No.5,837,247, Xu et al., Methods Enzymol. 326:376-418 (2000)), maltosebinding protein which binds an amylose substrate (U.S. Pat. No.5,643,758), cellulose binding domain from cellulase which bindscellulose (U.S. Pat. Nos. 5,962,289; 5,928,917; and 6,124,177) andHis-Tag (an oligopeptide) which binds a Nickel charged column. (VanDyke, et al. Gene 111:99-104 (1992)). In addition to the above,Glutathione S-transferase (GST) bind sepharose TM4B resin (Smith, D. B.,and Johnson, K. S. Gene 67:31-40 (1998)).

Each of the above affinity tags has certain limitations. For example,CBD irreversibly binds to chitin substrate and cannot be eluted undernon-denaturing conditions. However, CBD represents a potentially usefulaffinity tag with widespread application since it is readily obtainedfrom any of a family of enzymes identified as chitinases that arecapable of hydrolyzing chitin. As might be expected, chitinases areproduced by a diverse range of organisms that either contain chitin orrely on chitin as a food source. These organisms include bacteria,fungi, plants and vertebrates. (Watanabe et al. J. Bacteriol.,176:4465-4472 (1994), Jolles et al., Chitin and Chitinases, BirkhäuserVerlag, Basel (1999); Hashimoto et al., J. Bacteriol. 182:3045-3054(2000)). CBD binds to chitin, a polysaccharide abundantly represented innature. It is found in many fungal cell walls, nematode and insectexoskeletons, and crustacean shells.

Chitinases are characterized by a chitin binding domain (CBD) and acatalytic domain. For example, Chitinase A1 which is produced byBacillus circulans WL-12 contains three discrete functional domains: anN-terminal family 18 catalytic domain, a tandem repeat of fibronectintype III-like domains and a C-terminal chitin-binding domain (FIG. 1)(Watanabe et al., supra (1994)). Moreover, since CBD is located withinthe chitinase at a site that is distinct from the catalytic domain, itnaturally lacks hydrolytic activity when isolated from the enzyme foruse as an affinity tag.

While CBD has a number of useful properties it lacks the property ofreversible binding to chitin under non-denaturing conditions whichlimits its general utility.

SUMMARY OF THE INVENTION

In an embodiment of the invention, a protein is provided that includes achitin binding domain (CBD) capable of reversibly binding a chitinsubstrate under selected non denaturing conditions. The chitin bindingdomain may be modified by having one or more mutated amino acids. Themutated amino acid may be an aromatic amino acid optionally positionedwithin a binding cleft of the CBD, for example, a tryptophan. In aparticular embodiment, the tryptophan corresponds to Trp 687 of B.circulans chitinase A2.

Selected conditions for reversibly binding a chitin binding domaininclude a change in one of: ionic concentration, pH, detergentconcentration, antagonist or agonist concentration. For example a changein ionic conditions may include a reduction in salt conditions.

In an additional embodiment of the invention, a method is provided forobtaining a chitin binding domain capable of reversible binding to achitin substrate under non-denaturing conditions where the methodincludes the steps of modifying at least one amino acid within the CBD,and determining whether the modified CBD is capable of reversiblybinding chitin under selected conditions. One type of modification is amutation of a portion of DNA sequence encoding the CBD followed byexpression of the DNA in a host cell. The mutation may be introducedinto the portion of the DNA sequence by substituting an existingoligonucleotide portion of the DNA sequence with an alternativeoligonucleotide which differs in that it contains a mutation at a targetsite. For example, the target site may be a tryptophan located in thebinding cleft of the CBD. When for example, the tryptophan issubstituted with a phenylalanine, the CBD is capable of reversiblebinding to chitin under non-denaturing conditions. For example,non-denaturing conditions include a change in any of: ionicconcentration; pH; detergent concentration; or antagonist or agonistconcentration.

In an additional embodiment of the invention, a method is provided forproducing and purifying a target protein molecule where the methodincludes the steps of: constructing a DNA expression vector whichexpresses a hybrid polypeptide in a transformed host cell, the hybridpolypeptide comprising the target protein molecule and a modified chitinbinding domain where the chitin binding domain has a specific andreversible affinity for a substrate such as chitin or derivatives oranalogues thereof; introducing the expression vector into an appropriatehost cell; expressing the hybrid polypeptide; contacting the hybridpolypeptide produced by the transformed cell with the substrate to whichthe CBD binds; and recovering the hybrid polypeptide. The hybridpolypeptide may for example be recovered from the substrate to which itis bound by altering the ionic condition or pH or by contacting thebound hybrid polypeptide with a detergent or an agonist or antagonistwhich displaces the hybrid polypeptide.

In an additional embodiment of the invention, a method is provided forpurifying a chitin binding domain-target molecule conjugate from amixture of molecules. The method includes the steps of adding to themixture, a substrate having a specific and reversible affinity for CBDso as to permit binding and immobilizing of the conjugate to thesubstrate; removing the bound conjugate from the mixture; and eluting inaltered ionic conditions, the conjugate from the substrate to obtain thepurified conjugate.

In an additional embodiment of the invention, a kit is provided forpurifying a recombinant protein, that includes a plasmid, the plasmidcontaining a DNA sequence encoding a modified CBD or portion thereof andan insertion site for inserting the DNA sequence encoding therecombinant protein; a substrate for specific and reversible binding ofthe fusion protein; and optionally a buffer for eluting the fusionprotein from the substrate.

In an embodiment of the invention, a vector within or separate from ahost cell is provided where the vector is capable of expressing amodified chitin binding domain (CBD) fused to a protein molecule to bepurified, the vector including a DNA fragment coding for the modifiedchitin binding domain or portion thereof, having a specific andreversible affinity for a substrate which binds to the chitin bindingprotein. The vector may further express an additional DNA fragmentcoding for the protein molecule to be purified where the additional DNAfragment is optionally located within or adjacent to the CBD sequence.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Amino acid sequence alignment of the chitin-binding domain fromBacillus circulans chitinase A1 with domains of other procaryoticchitinases. Sequences were aligned with the program CLUSTAL V (40).Conserved residues are indicated in black boxes. Amino acids sequencesshown are from: CBD of Bacillus circulans WL-12 chitinase A1 (B.circulans A1 (SEQ ID NO: 1)), Bacillus circulans WL-12 chitinase D (B.circulans ChiD (SEQ ID NO:2)), Aeromonas sp. Strain 10S-24 chitinase II(Aeromonas ChiII (SEQ ID NO:3)), Janthinobacterium lividum chitinase (J.lividum Chitinase (SEQ ID NO:4)), Serratia marcescens 2170 chitinase C(S. marcescens ChiC (SEQ ID NO:5)), Aeromonas sp. Strain 10S-24chitinase II (Aeromonas ChiII (SEQ ID NO:6)), Aeromonas sp. Strain 10SORF1 (Aeromonas ORF1 (SEQ ID NO:7)), Aeromonas sp. Strain 10S-24chitinase I (Aeromonas ChiI (SEQ ID NO:8)), Serratia marcescens 2170chitinase B (S. marcescens ChiB (SEQ ID NO:9)), Janthinobacteriumlividum chitinase (J. lividum Chitinase (SEQ ID NO:10)), Alteromonas sp.Strain O-7 chitinase 85 (Alteromonas Chi85 (SEQ ID NO:11)), Streptomycesgriseus chitinase C (S. griseus ChiC (SEQ ID NO: 12)), Vibrio harveyichitinase A (V. harveyi ChiA (SEQ ID NO:13)), Aeromonas caviaeextracellular chitinase A (A. cavia ChiA (SEQ ID NO:14)). The first fivesequences are considered to belong to the CBD_(ChiA1) group. The numberat the right of each sequence represents the position of the lastresidue in each sequence. The residues of CBD_(ChiA1) that were mutated,are indicated by a star above the sequence. The numbers at the toprepresent the position in B. circulans ChiA1.

FIG. 2. Schematic ribbon drawing of the CBD of Bacillus circulanschitinase A1.

FIG. 2A. Drawing of the wild-type CBD of Bacillus circulans chitinaseA1.

FIG. 2B. Drawing of the CBD harboring the W687F mutation. β-strands areshown as curved arrows in yellow. Secondary structure elements, N and Ctermini, and the mutated residues are labeled. Red color representsspecifically the residue in position 687. The sequence of Bacilluscirculans chitinase A1 was obtained from NCBI structures database andfigures were obtained using Swiss-Pdb Viewer version 3.7b1.

FIG. 3. Chitin binding activity of PXB mutant proteins. The mutated CBDwas expressed as a fusion protein (PXB, 56 kDa) consisting of theN-terminal paramyosin ΔSal fragment (P, 26:kDa), the Mxe GyrAmini-intein (X, 22 kDa) and the mutated CBD of Bacillus circulanschitinase A1 (B, 8 kDa).

FIG. 3A. A chitin binding assay for each PXB protein carrying an alaninesubstitution was carried out in Tris-buffer (pH 8) containing 50 mMNaCl.

FIG. 3B. A chitin binding assays were performed in buffer containingeither 50 mM NaCl (lanes 1-3) or 2 M NaCl (lanes 4-6) for the PXB mutantproteins carrying W687F.

FIG. 3C. A chitin binding assay for W687Y in different NaCl conditions(50 mM NaCl in lanes 1-3 and 2M NaCl in lanes 4-6).

FIG. 3D. A chitin binding assay for W687T in different NaCl conditions(50 mM NaCl in lanes 1-3 and 2M NaCl in lanes 4-6).

FIG. 3E. A chitin binding assay for P689F in different NaCl conditions(50 mM NaCl in lanes 1-3 and 2M NaCl in lanes 4-6).

The samples were analyzed by Coomassie Blue stained SDS-PAGE. Themutated amino acid and its position in the CBD are indicated on top ofeach gel. UI, uninduced cell extract. Lanes 1 and 4, clarified cellextract. Lanes 2 and 4, chitin flow-through. Lanes 3 and 6, a sample ofchitin beads following wash with the same buffer used for loading. BroadRange protein marker (kDa) is indicated on the left side of each gel.

FIG. 4A. Characterization of the W687F mutant. Chitin binding activityof PXB W687F mutant protein at various NaCl concentrations. Inducedcells were lysed in 20 mM Tris-buffer (pH 8) containing various NaClconcentrations indicated at the top of the gel. The samples wereanalyzed by Coomassie Blue stained SDS-PAGE. UI, uninduced cell extract.Lane 1, crude cell extract. Lane 2, flow-through. Lane 3, a sample ofchitin beads following wash with the appropriate buffer. Lanes 4 and 5,a fraction after elution with buffer containing 50 mM or no NaClfollowing loading and washing with buffer containing 2 M NaCl. Lane 6, asample after passage of the eluted fraction adjusted to 2 M NaCl over anew chitin resin. Lane 7, a sample of chitin beads after reloading andwashing with a buffer containing 2 M NaCl.

FIG. 4B. Elution curves of PXB W687F mutant at different saltconcentrations. Loading of the wild type PXB protein and of the W687Fmutant was carried out at 2 M NaCl. For the PXB W687F mutant, elutionswere achieved in 20 mM Tris (pH 8) containing either 50 mM NaCl (♦), 0.1M NaCl (□), 0.5 M NaCl (▴), or 1 M NaCl (◯). The elution of the wildtype PXB was performed at 50 mM NaCl (X).

FIG. 5. Purification of recombinant proteins fused to the ChBD carryingthe W687F mutation.

FIG. 5A. Schematic overview of the one-step affinity purification forrecombinant proteins fused to the CBD (W687F).

FIG. 5B. Purification of hGM-CSF-ChBD.

FIG. 5C. Purification of Her-2(KD)-ChBD.

The samples were analyzed by Coomassie Blue stained SDS-PAGE. Lane 1,uninduced cell extract. Lane 2, crude cell extract. Lane 3, supernatantfrom the crude cell extract after centrifugation. Lane 4, load ofrenatured proteins in 20 mM Tris buffer (pH 8) containing 2 M NaCl. Lane5, renatured proteins flow-through. Lane 6, a sample of chitin beadsafter loading renatured proteins. Lane 7, eluted protein from chitinbeads with 20 mM Tris-buffer (pH 8) containing 50 mM NaCl.

DETAILED DESCRIPTION OF THE EMBODIMENTS

The utility of CBD has been enhanced by modifications to the proteinthat cause the CBD to be capable of reversible binding to a chitinsubstrate under conditions that do not denature proteins (non-denaturingconditions).

The modified CBD may be linked to a protein or other molecule ofinterest whether covalently or by affinity binding or via a linkermolecule to form a molecular conjugate. Where the conjugate is presentin a mixture, it may be selectively bound to a CBD-specific substrateand eluted from the substrate under select conditions.

“Chitin binding domain”, “CBD” or ChBD here refers to any binding domainderived from a naturally occurring or recombinant chitinase, includingchitinases for which sequences are available from sequence databasessuch as GenBank to or contained within gene libraries made according tostandard molecular biology techniques (Sambrook et al., MolecularCloning: A Laboratory Manual, CSH 1989) using conserved sequence motifssuch as described in FIG. 1. FIG. 1 provides an example of sequencemotifs observed when 13 chitin binding domains from different sourceswere aligned. Examples of chitinases include at least 6 differentchitinases, A1, A2, B1, B2, C, and D present in Bacillus circulans WL-12(Watanabe et al., J. Bacteriol., 172:4017-4022 (1990); Watanabe et al.,J. Bacteriol., 176:4465-4472 (1994)) derived from four genes, chiA,chiB, chiC, and chiD, with chitinase A2 and B2 being generated byproteolytic modification of chitinase A1 and B1, respectively (Alam etal., J. Ferment. Bioeng., 82:28-36 (1996)).

A “target molecule” is a molecule of interest that includes anyprokaryotic or eukaryotic, simple or conjugated protein that can beexpressed by a vector in a transformed host cell and further includesproteins that may be subject to post translational modifications innatural or synthetic reactions.

The term “protein” is intended to include peptides and derivatives ofproteins or peptides and to further include portions or fragments ofproteins and peptides. Examples of proteins include enzymes includingendonucleases, methylases, oxidoreductases, transferases, hydrolases,lyases, isomerases or ligases, storage proteins, such as ferritin orovalbumin; transport proteins, such as hemoglobin, serum albumin orceruloplasmin; structural proteins that function in contractile andmotile systems, for instance, actin, myosin, fibrous proteins, collagen,elastin, alpha-keratin, glyco-proteins, virus-proteins andmuco-proteins; immunological proteins such as antigens or antigenicdeterminants which can be used in the preparation of vaccines ordiagnostic reagents; blood proteins such as thrombin and fibrinogen;binding proteins, such as antibodies or immunoglobulins that bind to andthus neutralize antigens; hormones and factors such as human growthhormone, somatostatin, prolactin, estrone, progesterone, melanocyte,thyrotropin, calcitonin, gonadotropin, insulin, interleukin 1,intereukin 2, colony stimulating factor, macrophage-activating factorand interferon; toxic proteins, such as ricin from castor bean orgrossypin from cotton linseed and synthetic proteins or peptides.

It is further envisioned that in addition to a protein expressed by avector, the target molecule may alternately be a non-protein,non-substrate molecule isolated from nature or made synthetically whichmay form a conjugate with CBD by means of covalent linkage subsequent tosynthesis or by non-covalent linkage (such as affinity binding). Atarget molecule also refers to a molecule which may bind to a proteincomplex formed between the affinity tag and a protein where the affinitytag binds to a substrate. The molecule may be any of: an organicmolecule or an inorganic molecule including a co-factor, ligand,protein, carbohydrate, lipid, synthetic molecule, ion, where theinorganic molecule further includes fluorophors and dyes or mixtures ofany of the above.

“Substrate” refers to any molecule to which CBD will bind. Thispreferably includes chitin which is an insoluble β-1,4-linkedhomopolymer of N-acetyl-D-glucosamine, P. Jolles et al. Chitin andchitinases, Birkhäuser Verlag (1999), Basel., but may also includechitin analogues and derivatives that are naturally occurring orprepared in part or wholly by chemical synthesis. The substrate may beformed into beads, colloids, columns, films, sponges, filters, coatingor other suitable surfaces for use in binding an affinity tag forpurposes that include isolation or purification of a target molecule oranalysis of the presence or amount of a target molecule in a diagnostictest format or for binding a marker as an indicator of a chemicalreaction or other use.

“Modified CBD” refers to any change to a CBD that results in its bindingto substrate being altered under select conditions where such alterationin binding would not occur in unmodified CBD.

“Selected condition(s)” refers to any condition which when applied to aconjugate of a target molecule and CBD bound to substrate via the CBD,causes reversal of binding. The selected condition is preferablyrequired to be of the type that does not degrade the target molecule.

“Host cells” refers to cells that express target molecules, CBD and/orfusion proteins and include any known expression system in prokayotes oreukaryotes including bacterial host cells, yeast, invertebrate, fish andmammalian cells including human cells

Desirable features of a Modified CBD

Desirable features of a modified CBD may include any or all of thefollowing:

-   -   (a) a size or other characteristics of the modified CBD should        preferably not interfere with the function of the target protein        to which it is associated. An advantage of non-interference is        that cleavage of the CBD from the protein is not required to        obtain purified active target protein. Indeed, where the size of        the affinity tag is less then about 30 kb or less than 20 kd,        interference with functionality of the target protein may be        minimized or avoided. Examples VII-IX show that CBD (about 6 Kd)        does not interfere with the function of a target recombinant        protein EK-CBD. In those circumstances where the target protein        is very small, a DNA sequence encoding a linking peptide        sequence may be inserted between DNA for the affinity tag and        the target peptide. The resultant fusion protein may be cleaved        by a proteolytic agent to liberate the target protein after        purification has been completed;    -   (b) an ability of the modified CBD to bind tightly to both a        substrate and the target protein under one set of conditions and        under a separate set of conditions, to maintain an association        with the target protein while being eluted from the substrate.        Example V shows how the binding of modified CBD to substrate can        be made energetically less favorable under selected conditions        by introducing mutations into the protein;    -   (c) an ability to recognize a substrate that is readily        available in nature or capable of cost effective manufacture and        may be formed into any of a variety of formats according to the        desired use such as beads or columns for purification of a        target molecules. FIG. 5A shows results of a one step chitin        column purification of hGM-CSF-CBD and Her-2(KD)-CBD (FIG. 5B        and 5C);    -   (d) Absence of properties that cause degradation of the        substrate by the modified CBD or target protein under the set of        conditions in which the substrate is used to separate the target        protein from a mixture. For example, the CBD lacks hydrolytic        activity associated with chitinase where chitinase digests        chitin.        Identifying a Suitable Modification of the Chitin Binding Domain        by Targeted Mutation of the DNA Sequence Encoding the CBD

Mutations in DNA which result in an altered amino acid sequence may berandom or may be targeted to a specific amino acid or amino acids. Onecriteria for selecting an amino acid target is the location of the aminoacid in the protein as determined by crystallographic data. For example,a targeted amino acid may be located on the surface of the CBD or withinthe binding cleft.

In one embodiment of the invention, targeted mutagenesis results inchanges to one or more amino acids in the 45 residues CBD selectedaccording to the tertiary structure of the protein. As shown in FIG. 2,CBD has a compact and globular structure containing two antiparallelp-sheets and a core region formed by hydrophobic and aromatic residues.Several residues that may be important for the hydrophobic interactionwith chitin may have one or more of the following properties: (i) theyare well conserved among different bacterial chitinases; (ii) they existon the surface of the molecule or in the hydrophobic core, and (iii)they are hydrophobic or aromatic amino acids with the potential to formhydrophobic interactions with chitin. For example, Trp⁶⁸⁷, Pro⁶⁸⁹ andPro⁶⁹³, are highly conserved among different bacterial chitinases andexist on the surface of the molecule with the potential to formhydrophobic interactions with chitin.

Using methods of targeted mutagenesis, such as described in Example I,any desired amino acid can be altered and the effect on binding of CBDto chitin measured under selected conditions. While the method oftargeted mutagenesis using mutagenesis linkers is effective, there aremany alternative approaches known to one of ordinary skill in the artfor targeted mutagenesis which may alternatively be used to modify CBD.In Example I, mutations of amino acids at positions 681, 682 and 687 inthe protein are described. However, the method of Example I could alsobe applied to mutating any other amino acid in the CBD. Once an alteredCBD has been formed, it may be assayed according to Example II in orderto determine whether the CBD is capable of reversible binding to itssubstrate.

In Example I, a mutant CBD with an altered amino acid at position 687was found to be capable of reversible binding to chitin when the nativeTryptophan which is a hydrophobic residue within the binding cleft ofCBD was replaced with phenylalanine. This finding however does notpreclude other amino acid substitutions at this location being effectivealthough substitution with alanine, tyrosine or threonine, appeared tocompletely abolish CBD binding to chitin (FIG. 3). Nor does this findingpreclude amino acid substitution at other locations in the protein.While not wishing to be bound by theory, it appears from the 3Dstructure of the CBD, that Trp687 lies in the binding surface formedbetween the two β-sheets and interacts directly with the chitin chainthrough hydrophobic interactions (FIG. 2) presumably involving aromaticring polarization. Hence, while mutation of Trp⁶⁸⁷ to phenylalaninestill permitted binding at 2 M NaCl where the benzene ring ofphenylalanine residue substituted for the indole ring of tryptophan,affinity of binding of CBD to chitin became altered so as to beresponsive to altered ionic strength. In contrast, replacement of Trp⁶⁸⁷with tyrosine abolished binding to the chitin substrate probably due tothe presence of a hydroxy-group on the phenyl ring that may interferewith the general hydrophobicity of the region.

Interestingly, mutation of Pro689 to phenylalanine in the CBD abolishedbinding to chitin while mutation to alanine showed no effect (FIGS. 3Aand 3E). Pro689 is positioned in the loop between βB₄ and βB₅ in closeproximity of Trp687. Due to the cyclic and rigid nature of itspyrolidine side group, introduction of phenylalanine in this positionprobably disturbs the positioning of Trp687 in the structure. Ourresults also indicate that single amino acid substitutions of Trp656 orTrp696 have no substantial effect on the chitin binding activity.

While hydrophobic amino acids have been initially targeted bymutagenesis, the findings do not preclude the possibility thatnon-hydrophobic amino acids in the CBD may be modified to providereversible binding of CBD to chitin under select conditions. Moreover,while Example I describes a particular mutation in the CBD of Bacilluscirculans chitinase A1, it is expected, based on evolution of CBD as aclass, that modification to a targeted amino acid in a CBD from onesource will cause a similar effect in CBDs in general.

Desirable modifications of CBD provide a high affinity of binding tochitin under one set of conditions with reversible binding under alteredconditions. For example the altered conditions may be a shift in ionicstrength of the elution buffer from one ionic strength to a greater orlesser ionic strength. For example, ionic strength may be altered bymodifying the NaCl concentration in the buffer. For example, whereasmodified CBD may bind irreversibly in a buffer having a saltconcentration, in the range of 0.2 M-3M, the modified CBD may be elutedwhen the salt concentration is altered to 0.1-1M NaCl. While the aboveranges overlap, it should be understood that it is intended thatdifferent concentrations of NaCl in buffer determine whether binding ofCBD to substrate is reversible or non-reversible. Example III describeshow in a buffer containing 2M NaCl, a modified CBD binds strongly tochitin while at a different salt concentration (50 mM NaCl), theaffinity for CBD for substrate is reduced permitting elution of CBD fromthe substrate (Example III and IV). Alternatively, instead of changingsalt conditions, pH may be changed to cause modified CBD to bereversibly bound to substrate. For example, CBD having a Try 687modified to phenylalanine binds strongly to chitin at a pH in the rangeof 6 to 11. However, no or very poor binding of the CBD to chitin occursat or below pH 5. Other selected conditions may include a change intemperature, change in detergent concentration or addition or removal ofcompetitive binding molecules such as agonists or antagonists forexample, oligopolysaccharide homologs of chitin or CBD analogs.

The formation of a conjugate of CBD with a target molecule may includeeither a covalent or non-covalent association between the componentmolecules. There are many methods known in the art for creating aconjugate. If the target molecule is a protein, the protein may becovalently linked to the CBD during recombinant synthesis in a hostcell. Accordingly, the DNA sequence corresponding to CBD or targetprotein may be contained within a plasmid or chromosomal DNA in a hostcell for expression of a fusion protein. In certain circumstances, thetarget protein may become covalently linked to the CBD after cleavage ofan intein or alternatively a target protein may be linked to a CBD posttranslationally by protein ligation or by other means (U.S. Pat. No.5,834,247; International Publication No. WO 00/47751 and WO 01/57183).

Genes coding for the various types of protein molecules including thosedescribed below may be obtained from a variety of prokaryotic oreukaryotic sources, such as plant or animal cells or bacteria cells. Thegenes can be isolated from the chromosomal material of these cells orfrom plasmids of prokaryotic cells by employing standard, well-knowntechniques. A variety of naturally occurring and synthetic plasmidshaving genes encoding many different protein molecules are nowcommercially available from a variety of sources. The desired DNA alsocan be produced from mRNA by using the enzyme reverse transcriptase.

Preparation of DNA fusion and expression vectors may be achieved asdescribed in the art (U.S. Pat. No. 5,643,748) or as described inExample I or by other means known in the art. For example, the followingprotocol may be followed:

I. Preparation of Fusion Vector

-   -   A) The DNA encoding for the desired binding protein is purified.    -   B) The DNA is inserted into a cloning vector such as pBR322 and        the mixture is used to transform an appropriate host such as E.        coli.    -   C) The transformants are selected, such as with antibiotic        selection or auxotrophic selection.    -   D) The plasmid DNA is prepared from the selected transformants.    -   E) The binding activity domain of the protein is determined and        convenient restriction endonuclease sites are identified by        mapping or created by standard genetic engineering methods.

II. Insertion of DNA Coding for the Protein Molecule into the FusionVector

-   -   A) The protein molecule gene is cloned by standard genetic        engineering methods.    -   B) The protein molecule gene is characterized, e.g. by        restriction mapping.    -   C) A DNA restriction fragment which encodes the protein molecule        is prepared.    -   D) The protein molecule DNA fragment is inserted in the binding        protein fusion vector so that an in-frame protein fusion is        formed between the DNA fragment coding for the modified CBD and        the DNA fragment coding for the protein molecule.    -   E) The vector containing this hybrid DNA molecule is introduced        into an appropriate host.

III. Expression and Purification of the Hybrid Polypeptide

-   -   A) The host cell containing the fusion vector is cultured.    -   B) Expression of the fused gene is induced by conventional        techniques.    -   C) A cell extract containing the expressed fused polypeptide is        prepared.    -   D) The hybrid polypeptide is separated from other cell        constituents using an affinity column having as a matrix a        substance to which the modified CBD part of the hybrid        polypeptide has a specific affinity.    -   E) The bound purified hybrid polypeptide can be recovered and/or        utilized by the following methods:        -   (1) if the protein molecule's biological activity is            maintained in its hybrid or fused configuration it may            recovered from the column by eluting under selected            conditions and used directly after elution in its hybrid            form;        -   (2) the protein molecule may be separated from the modified            CBD either before or after elution from the column by            proteolytic or chemical cleavage; and        -   (3) the column may be used as a bioreactor with the fusion            protein immobilized on the column, e.g. by contacting and            reacting the bound fusion protein with a substrate which            interacts with the biologically active portion of the            protein molecule.

Linking Sequence

A DNA fragment coding for a predetermined peptide may be employed tolink the DNA fragments coding for the binding protein and proteinmolecule. The predetermined peptide is preferably one which recognizedand cleaved by a proteolytic agent such that it cuts the hybridpolypeptide at or near the protein molecule without interfering with thebiological activity of the protein molecule. One such DNA fragmentcoding for a predetermined polypeptide is described in Nagai et al.,Nature 309:810-812 (1984). This DNA fragment has the oligonucleotidesequence: ATCGAGGGTAGG (SEQ ID NO:15) and codes for the polypeptideIle-Glu-Gly-Arg (SEQ ID NO: 16). This polypeptide is cleaved at thecarboxy side of the arginine residue using blood coagulation Factor Xa.As noted above the linking sequence, in addition to providing aconvenient cut site if such is required, may also serve as a polylinker,i.e. by providing multiple restriction sites to facilitate fusion of theDNA fragments coding for the target and binding proteins, and/or as aspacing means which separates the target and binding protein which, forexample, allows access by the proteolytic agent to cleave the hybridpolypeptide. Other examples of linkers include GATGACGATGACAAG (SEQ IDNO:45) coding for Asp-Asp-Asp-Asp-Lys (SEQ ID NO:46) which is cleaved byenterokinase I and CCGGGTGCGGCACACTCAC (SEQ ID NO:47) coding forPro-Gly-Ala-Ala-His-Tyr (SEQ ID NO:48) which is cleaved by Genenase I(New England Biolabs 2002/2003 Catalog, page 163; Beverly, Mass.). Otherlinkers not generally cleaved by a protease include a polyasparaginelinker which consists of 10 Asp amino acids and is encoded byAACAACAACAACAACAACAACAACAACAAC (SEQ ID NO:49) and a “kinker” linker fromM13 gene 3 protein with a Gly-Gly-Ser-Gly sequence.

The formation of a conjugate of modified CBD with the target moleculeprovides special advantages in purifying target molecules on a largescale or small scale. In Examples, VI-IX, the target molecule wasexpressed in host cells as a fusion protein with modified CBD. Thefusion protein whether present in the production media or associatedwith the host cells which may be disrupted after harvesting, becomesimmobilized by binding to substrate. After removal of the unboundmaterial, the substrate to which the fusion protein is bound issubjected to non-denaturing conditions such as a particular ionicconcentration or pH causing the fusion protein to be released into aselected buffer. The insoluble substrate can then be removed byprecipitation, filtration or other standard techniques for removal ofparticles from a solution. Where the CBD does not interfere with thefunction of the target protein, cleavage of the CBD from the targetprotein is not required.

The above approach finds application in the purification of secretedproteins in microbial fermentation. Whereas purification of secretedproteins have the advantage of avoiding breaking the host cells prior torecovery, the desired secreted proteins may be present in large volumesof growth media. Handling large volumes of growth media presents a setof problems for which a solution would be desirable. For example, theyeast Kluyveromyces lactis is an important organism for industrial scaleproduction of proteins. For over a decade, K. lactis has been used forheterologous protein production in the food industry due to its abilityto grow to high cell density and secrete large amounts of recombinantprotein. A drawback to the protein secretion method is that typicallylarge volumes of culture medium must be processed to obtain highlypurified recombinant protein. To demonstrate one approach to this, wehave shown how secreted bovine enterokinase-CBD fusion protein can bepurified from batch harvests using a mutant version of the Bacilluscirculans chitinase A1 CBD as an affinity tag (Examples VII-IX).

The ability to alter the chitin binding domain from chitinase, so as tomake its binding to substrate reversible significantly enhances theutility of this protein for purification of target molecules fromdifferent environments including from simple or complex mixtures ofmolecules in small or large liquid volumes.

The present invention is further illustrated by the following Examples.These Examples are provided to aid in the understanding of the inventionand are not construed as a limitation thereof.

The references cited above and below are herein incorporated byreference.

EXAMPLE I Plasmid Construction

The vector pPXB expresses a tripartite fusion protein consisting of theDirofilaria immitis paramyosin ΔSa/I fragment (Steel et al., J.Immunol., 145:3917-3923 (1990)) followed by the Mxe GyrA intein ofMycobacterium xenopi (Mxe intein) and the wild type CBD from Bacilluscirculans WL-12 fused to the C-terminus of the intein (Evans et al.,Biopolymers 51:333-342 (1999a)). The sequence encoding humangranulocyte-macrophage colony-stimulating factor (hGM-CSF) (Cantrell etal., Proc. Natl. Acad. Sci. USA, 82:6250-6254 (1985); Mingsheng et al.,J. Biotechnol. 1995:157-162 (1995)) was amplified by polymerase chainreaction (PCR) using hGM-CSF cDNA (ATCC-39754) as template and theprimers: 5′-CTC GAGCATATGGCACCCGCCCGCTCGC-3′ (SEQ ID NO:17) and5′-CGTGGTTGCTCTTCCGCACTCCTGGACTGGCTCCCAGCAG-3′ (SEQ ID NO:18). Theresulting product was cloned into pTWIN1 vector (Evans et al., J. Biol.Chem., 274: 18359-18363 (1999b)) using NdeI and SapI sites yieldingpGM-CSF-XB. Expression of this construct produces hGM-CSF fused to theMxe intein-CBD. A HindIII site was introduced into the CBD wild typesequence by silent base substitution. To do this, the intein-CBD codingregion was amplified by PCR using Vent® DNA polymerase (New EnglandBiolabs, Inc.; Beverly, Mass.) and the following primers5′-AGATGCACTAGTTGCCCTAC-3′ (SEQ ID NO:19) and5′-TGTACGCTGCAGTTACAAGCTTGTGTGGGGCTGCAAACATTTAT-3′ (SEQ ID NO:20). Theresulting fragment was cloned in-frame in pPXB and pGM-CSF-XB vectorsusing the SpeI and PstI sites thereby replacing the original CBDsequence by a CBD with a 16 amino acid deletion of its C-terminus. Thefollowing oligonucleotides and their appropriate complement were used tointroduce the missing C-terminal residues into the HindIII and PstIsites in both vectors: W687F, 5′-AGCTTGGCAGGATTTGAACCATCCAACGTTCCTGCCTTGTGGCA GCTTCAATAACTGCA-3′ (SEQ ID NO:21);W687A/W696A, 5′-AGCTTGGCAGGAGCCGAACCATCCAACGTTCCTGCCTTGGCCCAGCTTCAATAACTGCA-3′ (SEQ ID NO:22);W687F/W696F, 5′-AGCTTGGCAGGATTTGAACCACCAACGTTCCTGCCTTGTTTCAGCTTCAATAACTGCA-3′ (SEQ ID NO: 23); W687T,5′-AGCTTGGCAGGAACCGAACCATCCAACGTT CTGCCTTGTGGCAGCTTCAATA ACTGCA-3′ (SEQID NO:24); W687Y, 5′-AGCTTGGCAGGATATGAACCATCCAACGTTCCTGCCT TGTGGCAGCTTCAATAACTGCA-3′ (SEQ ID NO:25); P689A,5′-AGCTTGGCAGGATGGGAAGCCTCCAACGTTCCTGCCTTGTGGCAGCTTC AATAACTGCA-3′ (SEQID NO:26); P689F, 5′-AGCTTGGCAGGATGGGAATTTTCCAACGTTCCTGCCTTGTGGCAGCTTCAATAACTGCA-3′ (SEQ ID NO:27);P693A, 5′-AGCTTGGCAGGATGGGAACCATCCAACGTTGCCGCCTTGTGGCAGCTTCAATAACTGCA-3′ (SEQ ID NO:28); P693F,5′-AGCTTGGCAGGATGGGAACCATCCAACGTTGC CTTGTGGCAGCTTCAATAACTGCA-3′ (SEQ IDNO:29); W696F, 5′-AGCTTGGC AGGATGGGAACCATCCAACGTTCCTGCCTTGTTTCAGCTTCAATAACTGCA-3′ (SEQ ID NO:30). The mutagenesis linkers were formed byannealing appropriate complementary oligonucleotides. Other CBDmutations were introduced into pGM-CSF-XB vector by linker replacementusing the AgeI and MfeI sites and the following oligonucleotides andtheir appropriate complement: W656A, 5′-CCGGTCTGAACTCAGGCCTCACGACAAATCCTGGTGTATCCGCTGCCCAGGTCAACACAG CTTATACTGCGGGAC-3′ (SEQ IDNO:31); W656F, 5′-CCGGTCT GAACTCAGGCCTCACGACAAATCCTGGTGTATCCGCTTTTCAGGTCAACACAGCTTATACTGCGGGAC-3′ (SEQ ID NO:32). Mutations in position 681 and682 into MfeI and HindIII sites were achieved using the followingoligonucleotides and their complement: H681A,5′-AATTGGTCACATATAACGGCAAGACGTAT AAATGTTTGCAGCCCGCCACA-3′ (SEQ IDNO:33); H681F, 5′-AA TTGGTCACATATAACGGCAAGACGTATAAATGTTTGCAGCCCTTTACA-3′(SEQ ID NO:34); T682A, 5′-AATTGGTCACATATAACGGCAAGACGTATAAATGTTTGCAGCCCCACGCA-3′ (SEQ ID NO:35). pGM-CSF-XB constructscontaining mutations were transferred into pPXB using SpeI and HindIIIsites. pGM-CSF-CBD vector was constructed by replacing the Mxe GyrAintein coding region in PGM-CSF-XB plasmid carrying the W687F mutationby a short linker using the SpeI and AgeI sites and the followingoligonucleotides and their appropriate complements: 5′-CTAGTGCCCGGGCCAA-3′ (SEQ ID NO:36). pCBD was constructed by replacement ofthe sequence coding for the paramyosin and the Mxe GyrA intein in pPXBcarrying the W687F mutation with a polylinker using the followingoligonucleotide and its appropriate complement: 5′-AGCTTGGCAGGATATGAACCATCCAACGTTCCTGCCTTGTGGCAGCTTCAATAACTGCA-3′ (SEQ ID NO:37). The polylinkerregion permits cloning of a gene of interest in-frame to the mutatedCBD. The sequence encoding the kinase domain of Her-2 [Her-2(KD)](Yamamoto et al., Nature 319:230-234 (1986)); Doherty et al., Proc.Natl. Acad. Sci. USA 96:10869-10874 (1999)) was amplified by PCR usingHuman Heart Marathon Ready cDNA (Clontech; Palo Alto, Calif.) and thefollowing primers: 5′-GGCTCTTCCATGCGGAGACTG CTGCAGGAAACGGAG-3′ (SEQ IDNO:38) and 5′-GGCTCTTC CGCCGCCCTGCTGGGGTACCAGATACTCCTC-3′ (SEQ IDNO:39). The resulting product was cloned into pCBD using the SapI siteyielding pHer-2(KD)-CBD vector. pHer-2(KD)-CBD expresses a two-partfusion protein consisting of the cytoplasmic kinase domain of the humanHer-2 protein [Her-2(KD)] fused at its C-terminus to the CBD harboringthe W687F mutation.

EXAMPLE II In Vitro Chitin-Binding Assay

Escherichia coli strain ER2566 (New England Biolabs, Beverly, Mass.;Chong et al., Gene 192:271-281 (1997)), harboring pPXB or its mutantderivatives, was grown at 37° C. in 1 liter of LB medium containing 100μg/ml of ampicillin to an A₆₀₀ of 0.5-0.7. The culture was induced with0.3 mM isopropyl-β-D-thiogalactoside (IPTG) at 30° C. for 3 hours or at16° C. overnight under the control of the T7 promoter (Studier et al.,Methods Enzymol., 185:60-89 (1990)). The proteins expressed from pPXBare referred to as PXB fusion proteins in our study. The binding assaywas carried out by resuspension of the cell pellet in 20 mM Tris-HCl (pH8) containing 2 M or 50 mM NaCl. Following sonication of the resuspendedcell pellet, debris was removed by centrifugation at 4,000× g for 30minutes. Clarified supernatants were loaded at 4° C. onto a column witha 3 ml bed volume of beads made of insoluble chitin (New EnglandBiolabs, Beverly, Mass.) previously equilibrated in the same buffer asthat used for resuspension. Equivalent amounts of load, flow-through,and a sample of chitin beads for each of the NaCl concentrations wereanalysed by electrophoresing a 12% Tris-glycine gel (Invitrogen,Carlsbad, Calif.) and staining with Coomassie Brilliant Blue forvisualisation.

EXAMPLE III Assay for NaCl-Dependent Chitin-Binding and Elution

Expression of the PXB (W687F) fusion protein was conducted as describedabove. Binding of the PXB (W687F) mutant protein to chitin was carriedout in 20 mM Tris-HCl (pH 8) containing either 2, 1, 0.5 or 0.05 M NaCl.Appropriate buffer was used for resuspension of the cell pellet and washof chitin resin after loading. For the elution assay, resuspension ofcell pellet and sonication were performed using the 20 mM Tris-HCl (pH8) buffer containing 2 M NaCl. After the centrifugation step of the cellextract, the supernatant was loaded onto a chitin column previouslyequilibrated with buffer containing 20 mM Tris-HCl (pH 8) and 2 M NaCl.The PXB protein was eluted with 20 mM Tris-HCl (pH 8) buffer containingeither 1 M, 0.5 M, 0.1 M or 50 mM NaCl. Thirty 1-ml fractions werecollected. NaCl concentration of the 50 mM NaCl-eluted fraction wasshifted back to 2 M in order to test whether binding was a reversiblephenomenon. Recombinant proteins for the NaCl-dependent chitin bindingand elution assay were subjected to SDS-PAGE analysis on 12%Tris-glycine gel and the protein concentration was determined byBradford assay (Bradford, Anal. Biochem., 72:248-254 (1976)) (Biorad,Cambridge, Mass.).

EXAMPLE IV Effect of CBD Mutations on Binding to Insoluble Chitin

In order to investigate the contribution of highly conserved residues ofchitinase Al CBD to chitin binding activity, single alaninesubstitutions were constructed in a 56 kDa fusion protein PXB possessinga C-terminal CBD as summarized in Table 1. The binding activities of thealanine replacement mutants were assayed by passage of the clarifiedinduced cell extract over chitin resin in a buffer containing 50 mMNaCl. SDS-PAGE was used to examine the binding efficiency by comparingthe load to the flow-through. In addition, a fraction of chitin resinwas also subjected to SDS-PAGE analyses after extensive washing of thecolumn. As shown in FIG. 3, all alanine mutant proteins, except theW687A and the W687A/W696A double mutants, bound efficiently to chitinresin as indicated by the absorption of most PXB by the chitin resinafter passage over the column (lane 2) and the presence of PXB speciesin the chitin resin fraction following a wash step (lane 3). Incontrast, the W687A and the W687A/W696A double substitutions abolishedthe chitin binding activity since the amount of PXB species was notsignificantly reduced in the cell extract after passage over the columnand was not present in the chitin resin fraction (W687A and W687A/W696A,lanes 2 and 3). Furthermore, the same pattern of binding was obtainedwhen binding assays were conducted with a 20 mM Tris-HCl buffercontaining 2 M NaCl (data not shown). Therefore, the data suggested thatW687 plays an important role in the interaction between CBD and chitin.

Based on structural modeling (FIG. 2), we reasoned that a conservativereplacement by a hydrophobic and aromatic residue such as phenylalaninemight compensate and mimic the role of W687. When the binding assay wasperformed in a buffer containing 50 mM NaCl, it appeared that thebinding profile for the PXB (W687F) mutant protein (lanes 2 and 3, FIG.3B) was similar to that of the alanine substitution mutant. The bindingassay was further performed in a buffer containing 2 M NaCl to assesswhether interaction of the mutant proteins to chitin could be affectedby ionic strength since higher salt concentration might enhancehydrophobic interaction and therefore increase the binding efficiency ofthe CBD to chitin. Under high salt conditions, the PXB protein harboringthe W687F mutation (lanes 5 and 6, FIG. 3B) was functionally active andbound chitin as indicated by a significant decrease of the PXB (W687F)species in the flow-through (lane 5) and its presence in the chitinresin fraction (lane 6). The results suggested that binding activity canbe restored by the introduction of a phenylalanine residue at position687 with a concomitant increase in NaCl concentration. On the otherhand, replacement of W687 with tyrosine appeared to interfere withbinding to chitin possibly due to an additional hydroxy group on thephenyl ring. The binding of the W687Y mutant was noticeably decreased inthe reaction mixture containing either 50 mM or 2 M NaCl (FIG. 3C). Thelow affinity of this PXB species for chitin was evident since most ofthe mutant protein remained in the extract after passage over chitinresin at both 50 mM and 2 M NaCl concentration (lanes 2 and 5) and wasabsent in the sample of chitin beads (lanes 3 and 6). Furthermore,replacement of Trp687 by a threonine residue also resulted in a failureto bind chitin (FIG. 3D).

Mutation of other hydrophobic and aromatic residues, W656, H681, P693and W696 to phenylalanine did not significantly affect the affinity tochitin in either 2 M or 50 mM NaCl (data not shown). However,introduction of a phenylalanine residue in place of Pro689 caused asubstantial decrease in the binding efficiency (FIG. 3E) compared to theP689A mutation, resulting in an increase of the mutant protein in chitinflow-through (lane 2) and little protein on the chitin resin (lane 3).The W687F/W696F double mutant TABLE 1 Characterization of chitin-bindingdomain mutants Percentage of chitin binding in various NaClconcentration Mutants 2 M 0.05 M WT >90 >90 W⁶⁵⁶A >90 >90 H⁶⁸¹A >90 >90T⁶⁸²A >90 >90 W⁶⁸⁷A <10 <10 E⁶⁸⁸A >90 >90 P⁶⁸⁹A >80 >90 P⁶⁹³A >80 >80W⁶⁹⁶A >80 >90 W⁶⁸⁷A/W⁶⁹⁶A <10 <10 W⁶⁵⁶F >90 >90 H⁶⁸¹F >90 >90 W⁶⁸⁷F >90<10 W⁶⁸⁷T <10 <10 W⁶⁸⁷Y <10 <10 P⁶⁸⁹F <10 <10 P⁶⁹³F >90 >90W⁶⁹⁶F >60 >90 W⁶⁸⁷F/W⁶⁹⁶F >80 <10 E⁶⁸⁸Q >90 >90showed essentially the same binding efficiency as the W687F mutant,suggesting that there was no cumulative effect between those tworesidues. Finally, substitution of Glu688, a conserved charged residueon the surface, with alanine or glutamine did not significantly affectthe binding to chitin at both low and high salt concentrations (FIG.3A). Thus, these conserved residues do not appear to be essential forchitin binding.

EXAMPLE V Effect of Ionic Strength on Chitin-Binding and Elution

To further analyze the effect of ionic strength on the affinity tochitin, binding of the W687F mutant was assessed in buffer containing 2M, 1 M, 0.5 M or 50 mM NaCl. As shown in FIG. 4A, the binding efficiencyof the W687F mutant correlated with the ionic strength of the buffer.Increasing the NaCl concentration from 50 mM to 0.5 M or 1 M resulted inpartial binding of PXB (W687F) protein, as indicated by the presence ofPXB in a sample of chitin resin after loading and washing (0.5 M and 1M, lane 3). In contrast, binding at 2 M NaCl concentration permittedefficient binding to chitin indicated by the presence of only a traceamount of the PXB species in the chitin flow-through (2 M, lane 2) andthe presence of PXB in the chitin resin fraction (2 M, lane 3).

The observation that the W687F mutant protein was incapable of bindingchitin in 50 mM NaCl implied that the elution of the bound CBD fusionprotein might be conducted by lowering NaCl concentration. Indeed, afterloading and washing at 2 M NaCl, PXB proteins were efficiently eluted inbuffer containing 50 mM or no NaCl (lanes 4 and 5, FIG. 4A). We furtherexamined whether the chitin binding activity of the W687F mutant isreversible by adjusting the NaCl concentration of the eluted proteinfrom 50 mM to 2 M NaCl. PXB fusion protein bound to chitin efficientlysince it was completely depleted in the chitin flow-through and waspresent in the chitin resin fraction (lanes 6 and 7, FIG. 4A).Furthermore, different ionic strengths were used for elution afterabsorption and wash in the buffer containing 2 M NaCl (FIG. 4B). In thecontrol experiment, the PXB protein possessing the wild type CBDexhibited a very weak elution with buffer containing 50 mM NaCl. Theassay of the W687F mutant showed that 50 mM NaCl was sufficient forrelease of the mutant protein from chitin. Although the protein waspartially eluted in buffers containing 0.1 to 1 M NaCl less protein wasreleased from chitin beads in correlation to the increase in ionicstrength.

EXAMPLE VI One-Step Affinity Purification of CBD Fusion Proteins

Modification of CBD for example using the CBD (W687F) mutant resulted inan elutable affinity tag for single column purification of recombinantproteins. A protein fused to the mutated CBD could be purified by chitinresin in a high salt buffer (e.g. 2 M NaCl) and released by simplyshifting the NaCl concentration in the elution buffer to 50 mM NaCl(FIG. 5A). This was further demonstrated using humangranulocyte-macrophage colony stimulating factor (hGM-CSF) and thekinase domain of Her-2 [Her-2 (KD)] both fused at their C-terminus tothe mutated chitin binding domain (FIG. 5B and FIG. 5C).

Expression of PGM-CSF-CBD or pHer-2(KD)-CBD in E. coli ER2566 cells wascarried out at 30° C. for 3 hours in the presence of 0.3 mM IPTG whencell-density reached an A₆₀₀ of 0.5-0.7. Induced cells were collected bycentrifugation and resuspended in 20 mM Tris-HCl (pH 8) containing 0.5 MNaCl. Both fusion proteins were found in inclusion bodies which wereisolated by breaking cells by sonication followed by centrifugation at15,000× g for 30 min. The proteins were then solubilized in 20 mMTris-HCl (pH 8) containing 0.5 M NaCl, 7 M Guanidine-HCl and 10 mM DTTand insoluble components were removed by centrifugation at 15,000× g for30 min. To renature insoluble fusion proteins, the supernatant wasdialyzed successively at 4° C. against 20 mM Tris-HCl (pH 8) and 0.5 MNaCl containing: 8 M urea, 10 mM DTT; 6 M urea, 1 mM DTT; 4 M urea, 1 mMDTT; 2 M urea, 0.1 mM oxidized glutathione, 1 mM reduced glutathione.Renatured fusion proteins were dialyzed twice against 20 mM Tris-HCl,0.5 M NaCl containing 0.1 mM oxidized glutathione, 1 mM reducedglutathione, and no urea. Insoluble components were removed bycentrifugation at 15,000× g for 30 min and the final NaCl concentrationwas increased to 2 M. Binding was performed by loading the supernatantonto a 25 ml chitin resin equilibrated in 20 mM Tris-HCl (pH 8)containing 2 M NaCl. The column was washed with 30 column volumes of thesame buffer and then flushed with the elution buffer containing 20 mMTris-HCl (pH 8) and 50 mM NaCl. Proteins were analyzed with a 12%Tris-glycine gel and the concentration was determined by Bradford assay.

Both hGM-CSF-CBD and Her-2(KD)-CBD fusion proteins were expressed in E.coli strain ER 2566 as inclusion bodies and consequently absent in theclarified cell extract after centrifugation (FIG. 5, lane 3). Aftersolubilization and renaturation steps, these fusion proteins remainedsoluble and were applied to chitin resin at 2 M NaCl. Analysis of chitinbeads after loading and washing at 2 M confirmed that both recombinantproteins were absorbed onto chitin (lane 6). Binding was approximately80% for hGM-CSF-CBD and essentially 100% for Her-2(KD)-CBD (lane 5).Analysis by SDS-PAGE showed a prominent and single band corresponding tothe expected hGM-CSF-CBD and Her-2(KD)-CBD fusion protein when a buffercontaining 50 mM NaCl was used to elute the bound fusion proteins (lane7). The obtained yields were 12.7 mg fusion protein per 1 liter cellculture for hGM-CSF-CBD and 4.5 mg per liter for Her-2(KD)-CBD.

EXAMPLE VII Method for Secreting and Purifying Bovine Enterokinase fromKluyveromyces Lactis

A DNA fragment encoding bovine enterokinase with a c-terminal mutant CBDfusion [EK-CBD(W275F)] was created by PCR amplification from a templateconsisting of a K. lactis expression vector containing enterokinase witha wild-type CBD fusion (pEK-CBD). The forward primer for amplificationwas 5′-CCGCTCGAGAAAAGAATTGTTGGTGGTTCTGATTCTAGA-3′ (SEQ ID NO:40) and thereverse primer 5′-ATAAGAATGCGGCCGCTCATTGAAGCTGCCACAAGGCAGGAACGTTGGATGGTTCAAATCCT GCC-3′ (SEQ ID NO:41).The reverse primer directs incorporation of a 2 bp mutation into the CBDregion (bold/underline) thus converting it from wild-type to the W275Fmutant form. To facilitate subcloning, forward and reverse primers alsocontained sequences for XhoI and NotI restrictions sites (singleunderline), respectively. PCR conditions consisted of Vent® DNApolymerase in 20 mM Tris-HCl (pH 8.8 at 25° C.) containing 10 mM KCl, 10mM (NH₄)₂SO₄, 4mM MgSO₄, and 0.1% Triton X-100. The reaction mixture (50μl total volume) contained 1 μM of each primer, 200 μM dNTPs and 60 ngof pEK-CBD. The reaction was initiated using a “hot start” procedureconsisting of incubation at 95° C. for 5 min then 80 ° C. for 1 min atwhich time 2 U Vent® DNA polymerase was added. Thermocycling wasperformed for 30 cycles of successive incubations at 95° C. for 30 s,59° C. for 30 s and 72° C. for 1 min, followed by a final 72° C.incubation for 5 min. The PCR product was purified via the QIAQuick PCRIsolation Kit (Qiagen Inc., Studio City, Calif.).

All of the purified DNA was cleaved with NotI and XhoI as follows:purified PCR product (30 μl) was mixed with 5 μl of 10× NEBuffer 3 (500mM Tris-HCl, 100 mM MgCl₂, 1 M NaCl, 10 mM dithiothreitol), 1 μl BSA (10mg/ml), 1 μl each of both NotI (20 U) and XhoI (20 U), and distilledwater (12 μl), followed by incubation at 37° C. for 2 h. The reactionwas terminated by heating to 65° C. for 10 min, and the cleaved DNApurified via the QIAQuick PCR Isolation Kit. The cleaved DNA was ligatedinto NotI-XhoI cleaved pGBN2 (an integration vector for K. lactisexpression) as follows: 500 ng of NotI-XhoI cleaved PCR product (3 μl)was mixed with 500 ng of NotI-XhoI cleaved pGBN2 (3 μl), 2 μl of 10×Ligation Buffer (500 mM Tris pH 7.5, 100 mM MgCl₂, 100 mMdithiothreitol, 5 mM ATP), 11 μl distilled water, and 1 μl (1 U) ofligase, and incubated for 15 h at 4° C. The ligation was desalted bymicrodialysis on a 0.025 μm membrane (Millipore Inc., Bedford, Mass.) atRT for 30 min. Ligated DNA (10 μl) was electroporated into E. coliER2268. E. coli was prepared for electroporation by growing 1 L of cellsto an optical density of 0.5 in L-broth. The cells were chilled on icefor 15 to 30 min then pelleted at 4° C. by centrifugation at 4000 rpmfor 10 min. The cell pellet was washed twice in sterile cold water andonce in cold 10% glycerol, then resuspended in 2 ml 10% glycerol to afinal cell concentration of ˜3×10¹⁰ cells per ml. Cells were stored in70 μl aliquots at −70° C. until needed. To electroporate DNA into E.coli, frozen cells were thawed on ice and mixed with 10 μl of themicrodialyzed ligation. The mixture was placed into a cold 0.2 cmelectroporation cuvette and a pulse of electricity (2.5 KV, 25 μF and200 Ohm) was applied to the cell mixture. The E. coli was immediatelydiluted with 1 ml L-broth, grown at 37° C. for 30 min, and plated onL-agar plates containing 100 μg/ml ampicillin. After overnightincubation, screening for colonies carrying plasmids that successfullyligated the PCR product (described above) was performed by growing 10 mlcultures (L-broth with 100 ug/ml ampicillin) from 10 singletransformants. Plasmid DNA was isolated from each culture using theQIAprep Spin Miniprep Kit from Qiagen Inc. (Studio City, Calif.). Cloneswith inserts were identified by digesting miniprep DNA as follows: 5 μl(1 μg) plasmid DNA was mixed with 5 μl of 10× NEBuffer 3 (500 mMTris-HCl, 100 mM MgCl₂, 1 M NaCl, 10 mM dithiothreitol), 1 μl BSA (10mg/ml), 1 μl each of both NotI (20 U) and XhoI (20 U), and 38 μldeionized water, followed by incubation at 37° C. for 2 h. Digested DNAswere subjected to electrophoresis through a 1% agarose gel inTris-Acetate-EDTA (TAE) buffer. Clones containing a 903 bp insert weresubjected to automated sequencing using pGBN2-specific primers5′-TCCGAGCTCAAAACAATGAGATTTCCTTCAAT TTTTACT-3′ (forward) (SEQ ID NO:42)and 5′-GCATGTATACAT CAGTATCTC-3′ (reverse) (SEQ ID NO:43) to confirmproper incorporation of the 2 bp mutation into the CBD region.

EXAMPLE VIII Secreted Expression of EK-CBD(W275F) in K. Lactis

To integrate DNA encoding EK-CBD(W275F) into the chromosome of K. lactisfor expression, clones of DNA encoding EK-CBD(W275F) in pGBN2 were firstlinearized by digestion with SacII as follows: 15 μl (3 μg) plasmid DNA,5 μl 10× NEBuffer 4 (200 mM Tris-acetate, 100 mM magnesium acetate, 500mM potassium acetate, 10 mM dithiothreitol), 2 μl (40 U) SacII , and 28μl deionized water were mixed and incubated at 37° C. for 4 h. Digestedvector was purified via the QIAQuick PCR Isolation Kit (Qiagen Inc.,Studio City, Calif.) and eluted in 30 μl deionized water. Linearized DNA(10 μl) was introduced into K. lactis GG799 and integrated into thegenome at the LAC4 locus. K. lactis was prepared for electroporation bygrowing 100 ml of cells to an optical density of 1.0 in YPD broth (10 gyeast extract, 20 g peptone and 1% dextrose per liter). The cells werechilled on ice for 10 min then pelleted at 4° C. by centrifugation at4000 rpm for 10 min. The pellet was washed with 100 ml sterile coldwater and with 5 ml sterile cold 1 M sorbitol, then resuspended in 0.1ml sterile cold 1 M sorbitol to a final volume of ˜0.3 ml. The cellswere stored on ice until use. To electroporate DNA into the preparedcells, 70 μl of K. lactis cell suspension was mixed with 10 μl ofpurified SacII digested expression vector. The mixture was placed into acold 0.2 cm electroporation cuvette and a pulse of electricity (1.5 KV,25 μF and 200 Ohm) was applied to the cell mixture. The cells wereimmediately diluted with 1 ml sterile cold 1 M sorbitol and placed onice for 10 min after which 1 ml of YPD was added and the cells grown at30° C. for 2 h. Cells were plated on YPD agar plates containing 200μg/ml G418 and colonies of integrants allowed to form by incubation at30° C. for 3 days. Secretion of EK-CBD(W275F) was achieved by growingintegrants in YPD broth for 24-96 h. Enterokinase proteolytic activityassociated with secreted EK-CBD(W275F) was assayed directly from culturemedium in a fluorogenic assay as follows: 50 μl of culture supernatantwas mixed with 50 μl of 2× assay buffer (875 μM fluorescent peptide(H-Gly-Asp-Asp-Asp-Asp-Lys-BNA (SEQ ID NO:44)), 17.6% DMSO, 125 mM TrispH 8.0) and incubated at RT for 5-30 min. Released fluorescence comparedto a standard reaction (50 μl YPD and 50 μl 2× assay buffer) wasmeasured with a Perkin Elmer (Emeryville, Calif.) LS50B LuminescenceSpectrophotometer with excitation and emission wavelengths of 337 nm and420 nm, respectively.

EXAMPLE IX Chitin Bead Affinity Purification of EK-CBD(W275F) Activity

EK-CBD(W275F) was purified directly from culture media using a batchmethod as follows: a 250 ml YPD-broth culture of a K. lactisEK-CBD(W275F) secreting strain was grown at 30° C. for 48 h. The culturewas cleared of cells by centrifugation at 4000 rpm for 10 min at 4 ° C.Cleared culture was adjusted to 2 M NaCl by addition of 29.22 g of solidNaCl to promote binding of EK-CBD(W275F) to chitin beads. New EnglandBiolabs (Beverly, Mass.) chitin bead suspension (5 ml) was added to thecleared culture and the beads were gently stirred for 2 hours at 4° C.The entire mixture was passed through an empty 23 cm×2.3 cm column tocollect the EK-CBD(W275F)-bound chitin beads. Collected beads werewashed by passing 75 ml of wash buffer (2 M NaCl, 20 mM Tris pH 7.4)through the column. EK-CBD(W275F) was eluted from the chitin beads bypassing 25 ml of elution buffer (50 mM NaCl, 20 mM Tris pH 7.4) throughthe column while collecting 0.5 ml fractions. Fractions were assayed forenterokinase activity as follows: 50 μl of a fraction was mixed with 50μl of 2× assay buffer (875 μM fluorescent peptide(H-Gly-Asp-Asp-Asp-Asp-Lys-βNA) (SEQ ID NO:45), 17.60/% DMSO, 125 mMTris pH 8.0) and incubated at RT for 5-30 min. Released fluorescencecompared to a standard reaction (50 μl elution buffer and 50 μl 2× assaybuffer) was measured with a Perkin Elmer (Emeryville, Calif.) LS50BLuminescence Spectrophotometer with excitation and emission wavelengthsof 337 nm and 420 nm, respectively. Fractions having activity werepooled and stored frozen at −20° C.

Although certain preferred embodiments of the present invention havebeen described, the spirit and scope of the invention is by no meansrestricted to what is described above. For example, within the generalmethod for secreting CBD-tagged enterokinase, it is also possible toexpress and purify other CBD-tagged proteins from both K. lactis as wellas from other yeast and fungi, or from other eukaryotic or prokaryoticsecretory or cytosolic expression systems.

1. A method for producing and purifying a target protein moleculecomprising: (a) constructing a DNA expression vector which expresses ahybrid polypeptide in a transformed host cell, the hybrid polypeptidecomprising the target protein molecule and a modified chitin bindingdomain having a specific and reversible affinity for a substrate whichbinds to the chitin binding domain; (b) introducing the expressionvector into an appropriate host cell and expressing the hybridpolypeptide; (c) contacting the hybrid polypeptide produced by thetransformed cell with the substrate to which the CBD binds; and (d)recovering the hybrid polypeptide.
 2. A method according to claim 1,wherein recovering the hybrid polypeptide comprises altering the ionicconditions.
 3. The method of claim 1, wherein recovery of the hybridpolypeptide further comprises: contacting the bound hybrid polypeptidewith a substance which displaces the hybrid polypeptide.
 4. A methodaccording to claim 2, wherein the altered ionic condition is a reductionin NaCl molarity.
 5. A method according to claim 1, wherein thesubstrate is chitin.
 6. A method for purifying a chitin bindingdomain-target molecule conjugate from a mixture of molecules in apreparation comprising: (a) adding to the preparation, a substratehaving a specific and reversible affinity for CBD so as to permitbinding and immobilizing of the conjugate to the substrate; (b) removingthe bound conjugate from the mixture into a buffer; and (c) altering theionic conditions in the buffer so as to elute the conjugate from thesubstrate into the buffer to obtain the purified conjugate.
 7. A methodaccording to claim 6, wherein the altered ionic conditions comprise achange in NaCl molarity.
 8. A method according to claim 6, wherein thesubstrate is chitin.